docs: add comprehensive architecture assessment and fix dependencies

Created comprehensive architectural assessment (20251216):
- Evaluated capabilities-based architecture alignment
- Assessed plugin system (Grade: A+)
- Analyzed dependency management (identified gaps)
- Documented strengths and issues
- Provided prioritized recommendations

Fixed missing capability dependencies in pyproject.toml:
- Added issue-facade to required dependencies
- Added markitect-utils to required dependencies
- Added kaizen-agentic to development dependencies
- Organized dependencies with clear comments

Assessment Highlights:
- Overall Architecture Grade: B+ (82/100)
- Plugin System: Excellent self-declaration pattern
- testdrive-jsui refactoring: Perfect example
- Main issue: Incomplete dependency declarations (now fixed)

Next Steps (per assessment):
1. ✅ Fix dependency management (completed in this commit)
2. Test fresh installation
3. Complete submodule migration for local capabilities
4. Document capability roles and usage

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

pyproject.toml

@@ -9,6 +9,7 @@ description = "Advanced Markdown engine for structured content"
 readme = "README.md"
 requires-python = ">=3.8"
 dependencies = [
+    # Core external dependencies
     "markdown-it-py",
     "PyYAML",
     "click>=8.0.0",
@@ -16,14 +17,21 @@ dependencies = [
     "jsonpath-ng>=1.5.0",
     "aiohttp>=3.8.0",
     "toml",
+
+    # Core capabilities (required for basic functionality)
     "release-management @ file:./capabilities/release-management",
-    "testdrive-jsui @ file:./capabilities/testdrive-jsui"
+    "testdrive-jsui @ file:./capabilities/testdrive-jsui",
+    "issue-facade @ file:./capabilities/issue-facade",
+    "markitect-utils @ file:./capabilities/markitect-utils"
 ]
 
 [project.optional-dependencies]
 capabilities = [
     "markitect-content @ file:./capabilities/markitect-content"
 ]
+development = [
+    "kaizen-agentic @ file:./capabilities/kaizen-agentic"
+]
 
 [project.scripts]
 markitect = "markitect.cli:main"